[English] 日本語
Yorodumi
- PDB-1pku: Crystal Structure of Nucleoside Diphosphate Kinase from Rice -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pku
TitleCrystal Structure of Nucleoside Diphosphate Kinase from Rice
ComponentsNucleoside Diphosphate Kinase I
KeywordsTRANSFERASE / nucleoside diphosphate kinase / rice
Function / homology
Function and homology information


nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / metal ion binding
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside diphosphate kinase 1
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHuang, J.-Y. / Chang, C.-Y. / Chang, T. / Chen, C.-J.
CitationJournal: J.Struct.Biol. / Year: 2005
Title: Crystal structure of nucleoside diphosphate kinase required for coleoptile elongation in rice (Oryza sativa L.).
Authors: Huang, J.Y. / Chang, T. / Chang, C.Y. / Chen, C.J.
History
DepositionJun 6, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 23, 2014Group: Experimental preparation
Revision 1.4Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoside Diphosphate Kinase I
B: Nucleoside Diphosphate Kinase I
C: Nucleoside Diphosphate Kinase I
D: Nucleoside Diphosphate Kinase I
E: Nucleoside Diphosphate Kinase I
F: Nucleoside Diphosphate Kinase I
G: Nucleoside Diphosphate Kinase I
H: Nucleoside Diphosphate Kinase I
I: Nucleoside Diphosphate Kinase I
J: Nucleoside Diphosphate Kinase I
K: Nucleoside Diphosphate Kinase I
L: Nucleoside Diphosphate Kinase I


Theoretical massNumber of molelcules
Total (without water)204,47412
Polymers204,47412
Non-polymers00
Water4,071226
1
A: Nucleoside Diphosphate Kinase I
B: Nucleoside Diphosphate Kinase I
C: Nucleoside Diphosphate Kinase I
D: Nucleoside Diphosphate Kinase I
E: Nucleoside Diphosphate Kinase I
F: Nucleoside Diphosphate Kinase I


Theoretical massNumber of molelcules
Total (without water)102,2376
Polymers102,2376
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17210 Å2
ΔGint-72 kcal/mol
Surface area34850 Å2
MethodPISA
2
G: Nucleoside Diphosphate Kinase I
H: Nucleoside Diphosphate Kinase I
I: Nucleoside Diphosphate Kinase I
J: Nucleoside Diphosphate Kinase I
K: Nucleoside Diphosphate Kinase I
L: Nucleoside Diphosphate Kinase I


Theoretical massNumber of molelcules
Total (without water)102,2376
Polymers102,2376
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17240 Å2
ΔGint-78 kcal/mol
Surface area34760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.951, 182.944, 188.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Nucleoside Diphosphate Kinase I / Nucleoside Diphosphate Kinase


Mass: 17039.490 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Plasmid: pHAT12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07661, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL12B211
SYNCHROTRONNSRRC BL17B221.1274
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 3, 2003
RIGAKU RAXIS IV2IMAGE PLATEMar 10, 2003
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.12741
ReflectionResolution: 2.5→25 Å / Num. all: 85648 / Num. obs: 81623 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.37 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 8.6
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 4.8 / % possible all: 75.1

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2626 8162 RANDOM
Rwork0.208 --
all0.242 85648 -
obs0.227 81623 -
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14352 0 0 226 14578

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more